Starting phenix.real_space_refine on Wed Aug 5 17:24:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3l_46537/08_2026/9d3l_46537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3l_46537/08_2026/9d3l_46537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d3l_46537/08_2026/9d3l_46537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3l_46537/08_2026/9d3l_46537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3l_46537/08_2026/9d3l_46537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3l_46537/08_2026/9d3l_46537.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 248 5.49 5 S 14 5.16 5 C 6135 2.51 5 N 2060 2.21 5 O 2537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10994 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 785 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 704 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 90, 694 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 90, 694 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 693 Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 795 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 800 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 789 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 104, 789 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 787 Chain: "H" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 684 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "J" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2564 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "I" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2520 Classifications: {'DNA': 124} Link IDs: {'rna3p': 123} Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS D 82 " occ=0.57 ... (18 atoms not shown) pdb=" NE2BHIS D 82 " occ=0.43 residue: pdb=" N AARG G 32 " occ=0.58 ... (20 atoms not shown) pdb=" NH2BARG G 32 " occ=0.42 Time building chain proxies: 2.61, per 1000 atoms: 0.24 Number of scatterers: 10994 At special positions: 0 Unit cell: (89.76, 115.005, 117.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 248 15.00 O 2537 8.00 N 2060 7.00 C 6135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 224.0 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 9 sheets defined 69.3% alpha, 2.9% beta 114 base pairs and 213 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.501A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.717A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.515A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 3.512A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.513A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.611A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.599A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.551A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.328A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 56 through 84 removed outlier: 3.678A pdb=" N GLY H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.612A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.960A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.303A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.004A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.662A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.005A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.346A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 386 hydrogen bonds defined for protein. 1148 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 291 hydrogen bonds 582 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 213 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2137 1.33 - 1.45: 3697 1.45 - 1.57: 5339 1.57 - 1.69: 494 1.69 - 1.81: 26 Bond restraints: 11693 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DT I 71 " pdb=" C2' DT I 71 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" CA ASN C 73 " pdb=" C ASN C 73 " ideal model delta sigma weight residual 1.522 1.567 -0.044 1.37e-02 5.33e+03 1.05e+01 bond pdb=" C3' DT I 30 " pdb=" C2' DT I 30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT J 44 " pdb=" C2' DT J 44 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 11688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 14988 1.24 - 2.49: 1604 2.49 - 3.73: 236 3.73 - 4.98: 23 4.98 - 6.22: 10 Bond angle restraints: 16861 Sorted by residual: angle pdb=" O4' DG J -70 " pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 108.00 111.30 -3.30 7.00e-01 2.04e+00 2.22e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT J -59 " pdb=" C4 DT J -59 " pdb=" O4 DT J -59 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 16856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.68: 4661 28.68 - 57.36: 1602 57.36 - 86.04: 141 86.04 - 114.72: 1 114.72 - 143.40: 2 Dihedral angle restraints: 6407 sinusoidal: 4224 harmonic: 2183 Sorted by residual: dihedral pdb=" C4' DA I -45 " pdb=" C3' DA I -45 " pdb=" O3' DA I -45 " pdb=" P DA I -44 " ideal model delta sinusoidal sigma weight residual -140.00 3.40 -143.40 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DT J 44 " pdb=" C3' DT J 44 " pdb=" O3' DT J 44 " pdb=" P DT J 45 " ideal model delta sinusoidal sigma weight residual 220.00 89.31 130.69 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1228 0.040 - 0.079: 540 0.079 - 0.119: 139 0.119 - 0.158: 17 0.158 - 0.198: 2 Chirality restraints: 1926 Sorted by residual: chirality pdb=" CB THR D 119 " pdb=" CA THR D 119 " pdb=" OG1 THR D 119 " pdb=" CG2 THR D 119 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" P DA I -44 " pdb=" OP1 DA I -44 " pdb=" OP2 DA I -44 " pdb=" O5' DA I -44 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1923 not shown) Planarity restraints: 1278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO D 103 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 73 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C ASN C 73 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN C 73 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS C 74 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J -13 " 0.026 2.00e-02 2.50e+03 1.19e-02 3.89e+00 pdb=" N9 DA J -13 " -0.028 2.00e-02 2.50e+03 pdb=" C8 DA J -13 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA J -13 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA J -13 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA J -13 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA J -13 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA J -13 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA J -13 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA J -13 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA J -13 " -0.003 2.00e-02 2.50e+03 ... (remaining 1275 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 340 2.67 - 3.22: 8963 3.22 - 3.78: 20563 3.78 - 4.34: 27830 4.34 - 4.90: 39348 Nonbonded interactions: 97044 Sorted by model distance: nonbonded pdb=" OE2 GLU C 61 " pdb=" OG SER L 365 " model vdw 2.107 3.040 nonbonded pdb=" OE1 GLU C 61 " pdb=" NH1 ARG L 367 " model vdw 2.173 3.120 nonbonded pdb=" OH TYR G 39 " pdb=" OE2 GLU H 71 " model vdw 2.247 3.040 nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG K 367 " model vdw 2.266 3.120 nonbonded pdb=" N ALA G 14 " pdb=" OP1 DT I -42 " model vdw 2.267 3.120 ... (remaining 97039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'E' and resid 43 through 134) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 14 through 31 or resid 33 through 117)) selection = (chain 'G' and (resid 14 through 31 or resid 33 through 73 or (resid 74 and (nam \ e N or name CA or name C or name O or name CB )) or resid 75 through 117)) } ncs_group { reference = (chain 'D' and (resid 36 through 81 or resid 83 through 123)) selection = (chain 'H' and (resid 36 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 81 or resid 83 through 123)) } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.200 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11693 Z= 0.520 Angle : 0.804 6.222 16861 Z= 0.693 Chirality : 0.045 0.198 1926 Planarity : 0.005 0.068 1278 Dihedral : 28.951 143.404 4999 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.93 % Allowed : 26.06 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.30), residues: 738 helix: 0.95 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -0.66 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 71 TYR 0.017 0.002 TYR D 40 PHE 0.010 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.52 (11693) covalent geometry : angle 0.80438 / 0.69 (16861) hydrogen bonds : bond 0.13150 / 8.51 ( 677) hydrogen bonds : angle 4.80314 / 3.43 ( 1730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.261 Fit side-chains REVERT: G 91 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: H 99 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.8005 (mtt180) outliers start: 18 outliers final: 16 residues processed: 133 average time/residue: 0.8252 time to fit residues: 115.5656 Evaluate side-chains 132 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.173952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119070 restraints weight = 27274.033| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.70 r_work: 0.3142 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11693 Z= 0.140 Angle : 0.653 6.450 16861 Z= 0.381 Chirality : 0.045 0.229 1926 Planarity : 0.005 0.055 1278 Dihedral : 30.890 141.723 3589 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.09 % Allowed : 25.24 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.31), residues: 738 helix: 1.57 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.45 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.014 0.001 TYR D 40 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.14 (11693) covalent geometry : angle 0.65350 / 0.38 (16861) hydrogen bonds : bond 0.04257 / 2.80 ( 677) hydrogen bonds : angle 3.18105 / 2.27 ( 1730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.344 Fit side-chains REVERT: A 65 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 95 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7546 (mtp-110) REVERT: C 73 ASN cc_start: 0.7890 (t0) cc_final: 0.7672 (m-40) REVERT: D 116 LYS cc_start: 0.8407 (tttp) cc_final: 0.7784 (tttm) REVERT: E 120 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8084 (mtt) REVERT: H 56 SER cc_start: 0.8915 (m) cc_final: 0.8647 (p) REVERT: H 99 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7957 (mtt180) REVERT: H 108 LYS cc_start: 0.8410 (tppt) cc_final: 0.8048 (mttt) outliers start: 19 outliers final: 8 residues processed: 123 average time/residue: 0.8362 time to fit residues: 108.3784 Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 115 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN C 104 GLN D 84 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117756 restraints weight = 31365.937| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.74 r_work: 0.3125 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11693 Z= 0.148 Angle : 0.620 6.207 16861 Z= 0.363 Chirality : 0.044 0.240 1926 Planarity : 0.005 0.057 1278 Dihedral : 30.872 141.825 3568 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.93 % Allowed : 25.41 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.30), residues: 738 helix: 1.92 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.36 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.013 0.001 TYR D 40 PHE 0.011 0.001 PHE A 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (11693) covalent geometry : angle 0.61960 / 0.36 (16861) hydrogen bonds : bond 0.04289 / 2.85 ( 677) hydrogen bonds : angle 3.06491 / 2.17 ( 1730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.185 Fit side-chains REVERT: A 65 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8615 (mp) REVERT: B 95 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7598 (mtp-110) REVERT: D 116 LYS cc_start: 0.8425 (tttp) cc_final: 0.7820 (tttm) REVERT: H 56 SER cc_start: 0.9002 (m) cc_final: 0.8716 (p) REVERT: H 99 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.8011 (mtt180) REVERT: H 108 LYS cc_start: 0.8403 (mppt) cc_final: 0.7992 (mttt) outliers start: 18 outliers final: 8 residues processed: 127 average time/residue: 0.7758 time to fit residues: 103.7054 Evaluate side-chains 115 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.172972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117398 restraints weight = 23074.174| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.49 r_work: 0.3155 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11693 Z= 0.159 Angle : 0.623 6.496 16861 Z= 0.361 Chirality : 0.044 0.242 1926 Planarity : 0.005 0.053 1278 Dihedral : 30.895 141.111 3565 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.58 % Allowed : 23.78 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.31), residues: 738 helix: 2.00 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.41 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.012 0.001 TYR D 40 PHE 0.011 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (11693) covalent geometry : angle 0.62289 / 0.36 (16861) hydrogen bonds : bond 0.04098 / 2.72 ( 677) hydrogen bonds : angle 3.00691 / 2.13 ( 1730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.189 Fit side-chains REVERT: A 65 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8606 (mp) REVERT: A 122 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8310 (ptpp) REVERT: B 95 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7793 (mmm160) REVERT: D 116 LYS cc_start: 0.8554 (tttp) cc_final: 0.7907 (tttm) REVERT: E 120 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8152 (mtt) REVERT: G 91 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: H 56 SER cc_start: 0.9048 (m) cc_final: 0.8765 (p) REVERT: H 99 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.8136 (mtt180) REVERT: H 108 LYS cc_start: 0.8516 (mppt) cc_final: 0.8083 (mttt) REVERT: H 120 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7814 (mtpt) outliers start: 22 outliers final: 8 residues processed: 125 average time/residue: 0.8734 time to fit residues: 114.6705 Evaluate side-chains 118 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117760 restraints weight = 23037.396| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.48 r_work: 0.3162 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11693 Z= 0.150 Angle : 0.618 6.698 16861 Z= 0.358 Chirality : 0.044 0.242 1926 Planarity : 0.004 0.054 1278 Dihedral : 30.891 141.021 3565 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.09 % Allowed : 24.10 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.31), residues: 738 helix: 2.11 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.37 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.012 0.001 TYR D 40 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (11693) covalent geometry : angle 0.61789 / 0.36 (16861) hydrogen bonds : bond 0.04004 / 2.66 ( 677) hydrogen bonds : angle 2.98122 / 2.11 ( 1730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.253 Fit side-chains REVERT: A 65 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8591 (mp) REVERT: A 122 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8265 (ptpp) REVERT: B 95 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7915 (mmm160) REVERT: D 116 LYS cc_start: 0.8518 (tttp) cc_final: 0.7857 (tttm) REVERT: F 84 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8747 (mmm) REVERT: G 91 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: H 56 SER cc_start: 0.9052 (m) cc_final: 0.8750 (p) REVERT: H 99 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.8121 (mtt180) REVERT: H 108 LYS cc_start: 0.8467 (mppt) cc_final: 0.8008 (mttt) REVERT: H 120 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7724 (mtpt) outliers start: 19 outliers final: 9 residues processed: 124 average time/residue: 0.9302 time to fit residues: 121.2298 Evaluate side-chains 118 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 51 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN C 104 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118803 restraints weight = 23084.593| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.46 r_work: 0.3162 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11693 Z= 0.146 Angle : 0.612 7.024 16861 Z= 0.356 Chirality : 0.044 0.240 1926 Planarity : 0.004 0.053 1278 Dihedral : 30.878 140.839 3565 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.58 % Allowed : 22.80 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.31), residues: 738 helix: 2.16 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.33 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 71 TYR 0.015 0.001 TYR H 40 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (11693) covalent geometry : angle 0.61198 / 0.36 (16861) hydrogen bonds : bond 0.03941 / 2.61 ( 677) hydrogen bonds : angle 2.96146 / 2.09 ( 1730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.299 Fit side-chains REVERT: A 65 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8591 (mp) REVERT: A 122 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8326 (ptpp) REVERT: D 116 LYS cc_start: 0.8555 (tttp) cc_final: 0.7913 (tttm) REVERT: E 120 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8087 (mtt) REVERT: G 91 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: H 56 SER cc_start: 0.9030 (m) cc_final: 0.8752 (p) REVERT: H 84 ASN cc_start: 0.8435 (m-40) cc_final: 0.8210 (m-40) REVERT: H 99 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8153 (mtt90) REVERT: H 108 LYS cc_start: 0.8507 (mppt) cc_final: 0.8070 (mttt) REVERT: H 120 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7779 (mtpt) outliers start: 22 outliers final: 9 residues processed: 121 average time/residue: 0.9007 time to fit residues: 114.6983 Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 85 optimal weight: 10.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.172995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116967 restraints weight = 30804.488| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.74 r_work: 0.3121 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11693 Z= 0.159 Angle : 0.619 7.477 16861 Z= 0.357 Chirality : 0.044 0.218 1926 Planarity : 0.005 0.054 1278 Dihedral : 30.878 140.747 3561 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.61 % Allowed : 24.27 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.30), residues: 738 helix: 2.14 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.33 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 71 TYR 0.012 0.002 TYR D 40 PHE 0.011 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (11693) covalent geometry : angle 0.61925 / 0.36 (16861) hydrogen bonds : bond 0.04116 / 2.73 ( 677) hydrogen bonds : angle 2.96198 / 2.10 ( 1730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.308 Fit side-chains REVERT: A 65 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8543 (mp) REVERT: A 122 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8274 (ptpp) REVERT: B 95 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7908 (mmm160) REVERT: C 73 ASN cc_start: 0.8080 (t0) cc_final: 0.7672 (m110) REVERT: D 116 LYS cc_start: 0.8459 (tttp) cc_final: 0.7828 (tttm) REVERT: E 56 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8234 (ttmm) REVERT: E 120 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8399 (mtt) REVERT: G 91 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: H 56 SER cc_start: 0.8959 (m) cc_final: 0.8700 (p) REVERT: H 84 ASN cc_start: 0.8340 (m-40) cc_final: 0.8137 (m-40) REVERT: H 99 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.8038 (mtt180) REVERT: H 108 LYS cc_start: 0.8426 (mppt) cc_final: 0.8016 (mttt) REVERT: H 120 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7817 (mtpt) outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 0.9531 time to fit residues: 122.0054 Evaluate side-chains 122 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 69 optimal weight: 50.0000 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 104 GLN E 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.171619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116742 restraints weight = 27939.937| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.60 r_work: 0.3105 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11693 Z= 0.188 Angle : 0.640 7.039 16861 Z= 0.365 Chirality : 0.045 0.225 1926 Planarity : 0.005 0.055 1278 Dihedral : 30.931 141.056 3561 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.77 % Allowed : 24.92 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.30), residues: 738 helix: 1.99 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.37 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 71 TYR 0.013 0.002 TYR D 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (11693) covalent geometry : angle 0.63968 / 0.36 (16861) hydrogen bonds : bond 0.04467 / 2.97 ( 677) hydrogen bonds : angle 3.02993 / 2.15 ( 1730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.281 Fit side-chains REVERT: A 65 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8498 (mp) REVERT: A 122 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8278 (ptpp) REVERT: B 95 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7897 (mmm160) REVERT: C 73 ASN cc_start: 0.8041 (t0) cc_final: 0.7663 (m110) REVERT: D 116 LYS cc_start: 0.8467 (tttp) cc_final: 0.7818 (tttm) REVERT: E 120 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8074 (mtt) REVERT: H 56 SER cc_start: 0.8939 (m) cc_final: 0.8697 (p) REVERT: H 99 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.8067 (mtt180) REVERT: H 120 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7803 (mtpt) outliers start: 17 outliers final: 9 residues processed: 122 average time/residue: 0.9330 time to fit residues: 119.5942 Evaluate side-chains 122 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.172669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118253 restraints weight = 24769.551| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.54 r_work: 0.3128 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11693 Z= 0.141 Angle : 0.624 6.828 16861 Z= 0.358 Chirality : 0.044 0.222 1926 Planarity : 0.005 0.053 1278 Dihedral : 30.934 141.044 3561 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.77 % Allowed : 25.24 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.31), residues: 738 helix: 2.13 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.33 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 71 TYR 0.013 0.002 TYR D 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (11693) covalent geometry : angle 0.62416 / 0.36 (16861) hydrogen bonds : bond 0.04139 / 2.74 ( 677) hydrogen bonds : angle 3.00976 / 2.13 ( 1730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.307 Fit side-chains REVERT: A 65 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8575 (mp) REVERT: A 122 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8400 (ptpp) REVERT: B 95 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8023 (mmm160) REVERT: C 73 ASN cc_start: 0.8098 (t0) cc_final: 0.7698 (m110) REVERT: D 116 LYS cc_start: 0.8563 (tttp) cc_final: 0.7903 (tttm) REVERT: E 56 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8515 (ttmm) REVERT: E 120 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8460 (mtt) REVERT: H 56 SER cc_start: 0.8992 (m) cc_final: 0.8729 (p) REVERT: H 99 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.8174 (mtt180) REVERT: H 120 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7766 (mtpt) outliers start: 17 outliers final: 9 residues processed: 118 average time/residue: 0.9400 time to fit residues: 116.5850 Evaluate side-chains 119 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 50.0000 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.171423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116569 restraints weight = 25706.431| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.54 r_work: 0.3114 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11693 Z= 0.195 Angle : 0.647 6.946 16861 Z= 0.367 Chirality : 0.045 0.226 1926 Planarity : 0.005 0.054 1278 Dihedral : 30.967 141.183 3561 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.12 % Allowed : 26.06 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.30), residues: 738 helix: 1.96 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.37 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 71 TYR 0.013 0.002 TYR D 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (11693) covalent geometry : angle 0.64734 / 0.37 (16861) hydrogen bonds : bond 0.04487 / 2.98 ( 677) hydrogen bonds : angle 3.03183 / 2.15 ( 1730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.308 Fit side-chains REVERT: A 65 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 122 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8377 (ptpp) REVERT: B 95 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8019 (mmm160) REVERT: C 73 ASN cc_start: 0.8105 (t0) cc_final: 0.7712 (m110) REVERT: D 116 LYS cc_start: 0.8572 (tttp) cc_final: 0.7908 (tttm) REVERT: E 56 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8518 (ttmm) REVERT: G 77 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6162 (ttt-90) REVERT: H 56 SER cc_start: 0.9008 (m) cc_final: 0.8751 (p) REVERT: H 99 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8201 (mtt180) REVERT: H 120 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7777 (mtpt) outliers start: 13 outliers final: 8 residues processed: 118 average time/residue: 0.9577 time to fit residues: 118.6429 Evaluate side-chains 120 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 50.0000 chunk 67 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.171766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116526 restraints weight = 20578.395| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.34 r_work: 0.3140 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11693 Z= 0.166 Angle : 0.639 6.824 16861 Z= 0.364 Chirality : 0.045 0.224 1926 Planarity : 0.005 0.053 1278 Dihedral : 30.970 141.171 3561 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.28 % Allowed : 25.57 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.30), residues: 738 helix: 1.99 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -0.36 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 71 TYR 0.014 0.002 TYR D 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (11693) covalent geometry : angle 0.63855 / 0.36 (16861) hydrogen bonds : bond 0.04357 / 2.89 ( 677) hydrogen bonds : angle 3.02361 / 2.14 ( 1730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4226.91 seconds wall clock time: 72 minutes 31.03 seconds (4351.03 seconds total)